Genome and transcriptome assembly

Genome and transcriptome assembly

Two of our most powerful tools to measure biological processes and the organisms involved are DNA- and RNA-sequencing. In many settings, assembly of reads is needed to identify and quantify the molecules they originated from. We are particularly interested in the algorithmically challenging cases where classical approaches break down.

Topics we address:

• Genome-scale haplotype reconstruction through long-read assembly
• Aneuploid and polyploid genome assembly and error correction
• Copy-number detection from gene to chromosome scales
• Development of long-read assembly algorithms for repeat rich genomes and regions
• Isoform reconstruction and relative abundance estimation in high-density genomes
• Assembling complete microbial genomes, i.e. full circle or telomere-to-telomere